GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2971943

Query DataSets for GSM2971943

Status

Public on Jun 07, 2019

Title

Input DNA

Sample type

SRA

Source name

Testis

Organism

Mus musculus

Characteristics

strain: PWD/Ph
age: 13-15 days post-partum
genotype: wild-type
antibody: N/A
sequencing technique: ChIP-Seq

Extracted molecule

genomic DNA

Extraction protocol

For H3K4me3 ChIP-Seq, nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by MNase digestion. After high speed spin soluble chromatin was removed and used for ChIP.
For H3K4me3 ChIP-Seq, libraries were prepared for sequencing using Bio Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 ul water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix and 14-18 cycles of PCR.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2500

Description

PWD wild-type; Input DNA

Data processing

H3K4me3 ChIP-Seq data were aligned to the reference mm10 genome using bwa 0.7.12 (Li 2013). H3K4me3 ChIP-Seq data were aligned to the reference mm10 genome using bwa 0.7.12 (Li 2013). Aligned BAM files were converted to BED files with bedtools (Quinlan and Hall 2010) and duplicate reads were discarded. NCIS (Liang and Keleş 2012) was used to determine the background correction ratio (rBG). MACS 2.1.0.20150731 (Zhang et al. 2008) was used with the following arguments to call peaks: --ratio {rBG} -g mm --bw 1000 --keep-dup all --slocal 5000 -t {ChIP bed file} -c {input bed file}.
genome build: mm10
processed data files format and content: For each SSDS experiment, the associated BAM file contains all paired end ssDNA reads identified for that sample. Custom BAM tags describe properties of each read pair used for ssDNA detection: it : ITR length uh : microhomology length os : microhomology offset mm : # mismatches DSB hotspots are provided in bedgraph format for each DMC1 SSDS sample. Background corrected hotspot strength is listed in the fourth column. A bedgraph file is provided for H3K4me3 ChIP-Seq peaks. This contains the mm10 coordinates of each H3K4me3 peak. Column 4 is peak strength.

Submission date

Jan 30, 2018

Last update date

Jun 07, 2019

Contact name

Kevin Brick

E-mail(s)

brickkm@mail.nih.gov, kevbrick@gmail.com, brickkm@niddk.nih.gov

Organization name

NIDDK

Department

GBB